Freesurfer

freesurfer@nmr.mgh.harvard.edu

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Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline
by Pedro Rosa 06 Jul '14

06 Jul '14

Dear Doug and Jorge, Once again thank you a lot for the help you provided. I ran the longitudinal pipeline (Freesurfer 5.1), the LME and the mri_glmfit (paired). However, I am in trouble now with the design matrix, with the contrasts and and also in understanding the results. I tried to follow the LME wiki page (https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels) and my design matrix looks like this: - Intercept (all ones) - Time (a 0 for each of the baseline scans, and the respective interval in months for the follow-up scans) - Zero for patients and one for controls - Time x Patients (controls had only zeros in this column, while patients had a zero for the baseline scan, and the interval in months in the follow-up scan) - Age (continuous) - Medication intake between scans (continuous) - Substance misuse (categorical) - Gender (categorical) Thus, I included the following contrasts (CM.C) 0 0 0 -1 0 0 0 0 0 0 0 1 0 0 0 0 , ran the F statistics with lme_mass_F and generated sig.mgh with fs_write_fstats for each of them. Afterwards, I substituted the sig.mgh from the mri_glmfit with the one provenient from the LME, and ran mri_glmfit-sim. The mri_glmfit FSGD had only two classes (cases and controls), and no ‘variable’; thus, I included two contrasts: 1 -1 and -1 1. Both cluster summaries (0 0 0 -1 0 0 0 sig.mgh included in the -1 1 folder; and 0 0 0 1 0 0 0 0 sig.mgh in the 1 -1 folder) showed the same exact surface (area) cluster in the left rostral middle frontal gyrus. Therefore, I started questioning if I designed the matrix and the contrasts properly. Are they correct? Furthermore, I am also in doubt about how to interpret the findings. I opened the cache.th13.abs.sig.masked.mgh in tkmedit both using pial and inflated surfaces (fsaverage), and three clusters emerged in the frontal lobe (find pictures attached). I am curious about why the mask and cluster summary show distinct results (e.g., three instead of one cluster), and if the blue in the color bar means that the group described in the fourth column of the matrix design (patients) showed longitudinal surface area decrease in this / these cluster(s) in contrast to controls. Also, in my case, what would be outputted in cache.th13.abs.y.ocn.dat? The mean values for thickness / surface for the cluster derived from the mri_glmfit, from the MatLab LME processing, or simply from the recon-all processing? I would deeply appreciate your help once again. Best wishes, Pedro Rosa. 8 P > M, Douglas Greve wrote: > > > > On 4/26/14 2:11 PM, Pedro Rosa wrote: > > > Thanks, Doug! > > > I looked at the examples on the wiki, and the Paired Analysis wiki page as well. > > > You mentioned I should include the categorical and continuous variables in the fsgd file for the mri_glmfit. It seems that one of my analyses includes few subjects, and then one of the class end up lacking a adequate range of continuous variables, and consequently the mri_glmfit finished with errors (this error no longer appears after I merged that problematic group with another). > > > Therefore I ask whether it would be fine to run the mri_glmfit without some (or all) the continuous or/an categorical variables, while they would of course be included in the LME ran in MatLab. > > > > > > > Yes, that is fine > > > Further, I would like to ask what the FMHM outputs represents? The FWHM refers to the width of a gaussian. It is measured as the average correlation between the residuals of neighboring vertices (the correaltion coef get transformed into the FWHM). Smoothing with a gaussian of a certain FWHM will induce correlation, but there can be correlation from other sources so the FWHM you get out is not necessarily that which you used to smooth the data with. > > > > doug > > > Regards, > > > Pedro Rosa. > > > > > > > > > On Wednesday, April 16, 2014 at 11:49 AM, Douglas N Greve wrote: > > > > > > > > > > > On 04/15/2014 10:34 PM, Pedro Rosa wrote: > > > > > Hi, Doug. > > > > > Thanks a lot! > > > > > The command would look like this: mri_glmfit-sim --glmdir > > > > > lh.thickness.Sch.glmdir --sim mc-z 10000 2 teste --sim-sign abs > > > > > --overwrite --cache 1.3 abs > > > > > It takes only a few seconds to run. > > > > > > > > > > > > > > > > > > The command is fine, but remove --sim mc-z 10000 2 teste. This tells it > > > > to do the simulation, which you don't need to do. It is overridden by > > > > the --cache flag. If they had occurred in the other order, you would be > > > > waiting days for the simulation to run. > > > > > I have a few questions about how to run it: > > > > > 1) How the single entry for each subject look like in the FSGD file? > > > > > > > > > > > > > > > > > > I'm not sure what you mean. Have you looked at the examples on the wiki? > > > > > > > > > > 2) How to define the voxel/vertex-wise used to define clusters (after > > > > > —sim, -log10( p)), and the voxel-wise threshold for the —cache option? > > > > > What is the difference between them? > > > > > > > > > > > > > > > > > > They are the same > > > > doug > > > > > > > > > > Thanks again, > > > > > Pedro Rosa. > > > > > > > > > > On Monday, April 14, 2014 at 3:29 PM, Douglas N Greve wrote: > > > > > > > > > > > > > > > > > On 04/14/2014 10:35 AM, Pedro Rosa wrote: > > > > > > > Dear Doug and Jorge, > > > > > > > I tried what you suggested and I think it work, although I have some > > > > > > > concerns. > > > > > > > I am working with a longitudinal study with two time-points for all > > > > > > > subjects, three categorical variables (group, substance abuse / > > > > > > > dependence and gender) and three continuous variables (interval > > > > > > > between scans, age and medication intake). > > > > > > > I generated a contrast with intercept + 7 betas for the LME, ran it > > > > > > > without any problem and saved the sig.mgh using > > > > > > > fs_write_fstats(F_lhstats,mri,’sig.mgh’,’sig’). > > > > > > > For the mri_glmfit I entered the same output from mri_surf2surf I used > > > > > > > for the LME (smoothed at 10mm), but I did not know how exactly to > > > > > > > enter the categorical and continuous variables, or which contrast to > > > > > > > use. > > > > > > > > > > > > > > > > > > > > > > > > > > I would do it as a paired-test (see the wiki). You may have to re-run > > > > > > mris_preproc with the --paired-diff flag, then smooth by 10mm. Use this > > > > > > as the input to mri_glmfit. Set up the FSGD with the categorical and > > > > > > continuous variables (note that the FSGD file will have only a single > > > > > > entry per subject). Create your contrasts and run mri_glmfit. Overwrite > > > > > > the sig.mgh with the one from LME. Then run mri_glmfit-sim with the > > > > > > --cache option (not permutation) > > > > > > > > > > > > I don't know what your contrast of interest is, so I can't help you > > > > > > there. In the end, it does not matter because you are overwriting the > > > > > > sig map anyway. You just need a contrast as a place holder. > > > > > > > > > > > > doug > > > > > > > > > > > > > The commmand was: mri_glmfit —y pval.mgh —sim perm 10000 0.05 sch > > > > > > > > > > > > > > I just tested creating a matrix with 24 columns > > > > > > > (Nclasses*(Nvariables+1) as suggested for DODS). > > > > > > > Afterwards I ran the mri_glmfit-sim (mri_glmfit-sim --glmdir > > > > > > > Sch-glmdir --sim mc-full 5 2 teste --sim-sign abs, and it finished > > > > > > > apparently without errors. > > > > > > > I attached the logs for both mri_glmfit and mri_glmfit-sim. > > > > > > > > > > > > > > That said, I have the following questions: > > > > > > > > > > > > > > 1) What does the FWHM procedure does? > > > > > > > 2) How should I decide which contrast to test if the mri_glmfit does > > > > > > > not consider the longitudinal design? > > > > > > > 3) Will the mri_glmfit-sim consider only the FMHM output from > > > > > > > mri_glmfit and sig.mgh from the LME, or also other outputs from the > > > > > > > mri_glmfit? > > > > > > > 4) Does the FWHM rely only on the images, and not on variables and > > > > > > > contrasts? > > > > > > > > > > > > > > Thank you very much! > > > > > > > Pedro Rosa. > > > > > > > > > > > > > > On Monday, March 31, 2014 at 10:53 PM, Pedro Rosa wrote: > > > > > > > > > > > > > > > Thanks, Doug! > > > > > > > > Should I run the mri_preproc and and smooth the output using > > > > > > > > mri_surf2surf with, let’s say, 10mm, and than run the LME normally in > > > > > > > > MatLab? > > > > > > > > Would this be problematic with a different smoothing procedure in > > > > > > > > mri_glmfit? > > > > > > > > How will mri_glmfit deal with the longitudinal design? Does this > > > > > > > > matter, or the FWHM would only be estimated on a average image of all > > > > > > > > time-points for all subjects? > > > > > > > > Regards, > > > > > > > > Pedro Rosa. > > > > > > > > > > > > > > > > On Sunday, March 30, 2014 at 3:51 PM, Douglas Greve wrote: > > > > > > > > > > > > > > > > > > > > > > > > > > I think I would just run mri_glmfit on your data to get the proper > > > > > > > > > directly structure and estimate of FWHM, then copy the sig file from > > > > > > > > > the mixed fx analysis into the glmfit folder for one of the > > > > > > > > > contrasts. Then run mri_glmfit-sim. > > > > > > > > > > > > > > > > > > doug > > > > > > > > > > > > > > > > > > > > > > > > > > > On 3/29/14 10:29 AM, Pedro Rosa wrote: > > > > > > > > > > Dear Doug and Jorge, > > > > > > > > > > Thank you very much for your help. > > > > > > > > > > I found another message in the list > > > > > > > > > > (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-November/034649…) > > > > > > > > > > > > > > > > > > > > in which you suggested a way of using MC in mri_glmfit-sim by > > > > > > > > > > creating “fake files”, which would not be read by the script. In > > > > > > > > > > this case, only the simulation would be run, and not the full > > > > > > > > > > statistics. The command would be something like this: > > > > > > > > > > - mri_glmfit-sim --glmdir $SUBJECTS_DIR --sim mc-full 5 2 teste > > > > > > > > > > --sim-sign abs > > > > > > > > > > I created a “fake” mri_glmfit.log, fwhm.dat and mask.mgh files as > > > > > > > > > > suggested by the older post. This would be fine, I believe, if only > > > > > > > > > > sig.mgh is read by the script. > > > > > > > > > > However, I get this message after running the command: > > > > > > > > > > > > > > > > > > > > [server:Long-T0-T2-Posproc/Vertex/Sch] pedrogomesrosa% > > > > > > > > > > mri_glmfit-sim --glmdir $SUBJECTS_DIR --sim mc-full 5 2 teste > > > > > > > > > > --sim-sign abs > > > > > > > > > > > > > > > > > > > > if: Expression Syntax. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Is it possible to do what I am trying to do? Does the residual > > > > > > > > > > errors at each location included in the sig.mgh, and, if necessary, > > > > > > > > > > how to compute it into image FWHM? > > > > > > > > > > > > > > > > > > > > Regards, > > > > > > > > > > > > > > > > > > > > Pedro Rosa. > > > > > > > > > > > > > > > > > > > > On Friday, March 28, 2014 at 2:38 PM, Douglas N Greve wrote: > > > > > > > > > > > > > > > > > > > > > Jorge, do you output the FWHM? > > > > > > > > > > > doug > > > > > > > > > > > > > > > > > > > > > > On 03/27/2014 03:14 PM, jorge luis wrote: > > > > > > > > > > > > Hi Pedro > > > > > > > > > > > > > > > > > > > > > > > > Sorry, right now the only multiple comparisons corrections > > > > > > > > > > > > implemented > > > > > > > > > > > > in lme are the original Benjamini and Hochberg (1995) FDR procedure > > > > > > > > > > > > (lme_mass_FDR) and a more recent and powerful two-stage FDR > > > > > > > > > > > > procedure > > > > > > > > > > > > (lme_mass_FDR2): > > > > > > > > > > > > > > > > > > > > > > > > Benjamini, Y., Krieger, A.M., Yekutieli, D. (2006). Adaptive linear > > > > > > > > > > > > step-up procedures that control the false discovery rate. > > > > > > > > > > > > Biometrika, > > > > > > > > > > > > 93, 491-507. > > > > > > > > > > > > > > > > > > > > > > > > In my experience, this procedure is as powerful to detect > > > > > > > > > > > > effects in > > > > > > > > > > > > neuroimage data as alternative corrections with strong control of > > > > > > > > > > > > the > > > > > > > > > > > > family-wise error rate (FWE). However it would be great if we could > > > > > > > > > > > > use an implementation of any multiple comparisons correction with > > > > > > > > > > > > strong control of the FWE (MC, RFT, ect...) for lme (FDR procedures > > > > > > > > > > > > only provide weak control). The residual errors at each location > > > > > > > > > > > > required to compute an estimate of the image FWHM can be obtained > > > > > > > > > > > > from > > > > > > > > > > > > the lme output. But an actual FWHM estimate is not currently saved. > > > > > > > > > > > > > > > > > > > > > > > > Best > > > > > > > > > > > > -Jorge > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > El Martes 25 de marzo de 2014 8:15, Pedro Rosa > > > > > > > > > > > > <pedrogomesrosa(a)gmail.com (mailto:pedrogomesrosa@gmail.com) <mailto:pedrogomesrosa@gmail.com> > > > > > > > > > > > > <mailto:pedrogomesrosa@gmail.com>> > > > > > > > > > > > > escribió: > > > > > > > > > > > > > > > > > > > > > > > > Dear Doug, > > > > > > > > > > > > Thank you very much! > > > > > > > > > > > > I will try what you suggested, although I am not sure if Jorge's > > > > > > > > > > > > stream outputs the FMHM, or if I would need to run the statistics > > > > > > > > > > > > from the beggining using in the terminal, and not in MatLab. > > > > > > > > > > > > Do you think Jorge could comment on this issue? > > > > > > > > > > > > Regards, > > > > > > > > > > > > Pedro Rosa. > > > > > > > > > > > > > > > > > > > > > > > > On Mar 24, 2014, at 12:44 PM, Douglas Greve > > > > > > > > > > > > <greve(a)nmr.mgh.harvard.edu (mailto:greve@nmr.mgh.harvard.edu) <mailto:greve@nmr.mgh.harvard.edu> > > > > > > > > > > > > <mailto:greve@nmr.mgh.harvard.edu> > > > > > > > > > > > > <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > In theory, it should be possible. I have not used Jorge's stream, > > > > > > > > > > > > so I > > > > > > > > > > > > don't know that much about it. Does it save an estimate of the > > > > > > > > > > > > FWHM? If > > > > > > > > > > > > so, then you can run mri_surfcluster passing it the p-value (ie, > > > > > > > > > > > > -log10(p)) map, the FWHM, the mask, and a voxel-wise threshold. > > > > > > > > > > > > This is > > > > > > > > > > > > what mri_glmfit-sim does, so you might check that script for > > > > > > > > > > > > mri_surfcluster command line options > > > > > > > > > > > > > > > > > > > > > > > > doug > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On 3/22/14 11:03 PM, Pedro Rosa wrote: > > > > > > > > > > > > > Dear list, > > > > > > > > > > > > > I ran the recon-all and the Freesurfer 5.1 longitudinal pipeline > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > in a structural MRI dataset and I would like to use Monte Carlo as > > > > > > > > > > > > the method for correction for multiple comparisons. However, the > > > > > > > > > > > > longitudinal LME tutorial includes only FDR correction > > > > > > > > > > > > (lme_mass_FDR2). > > > > > > > > > > > > > Is it possible to use Monte Carlo correction for longitudinal > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > data? Can I input the outputs from MatLab (fstats = > > > > > > > > > > > > lme_mass_F(?h,CM): stats.F / pval / sgn / df) into mri_glmfit and > > > > > > > > > > > > then run Monte Carlo? > > > > > > > > > > > > > If not, do you have any other suggestions of how I use Monte > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Carlo in longitudinal analyses? > > > > > > > > > > > > > Thanks in advance, > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > > > > > > Freesurfer mailing list > > > > > > > > > > > > Freesurfer(a)nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) > > > > > > > > > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > > > > > > > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > > > > > > > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > > > > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > The information in this e-mail is intended only for the person to > > > > > > > > > > > > whom it is > > > > > > > > > > > > addressed. 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Greve, Ph.D. > > > > > > > > > > > MGH-NMR Center > > > > > > > > > > > greve(a)nmr.mgh.harvard.edu (mailto:greve@nmr.mgh.harvard.edu) <mailto:greve@nmr.mgh.harvard.edu> > > > > > > > > > > > <mailto:greve@nmr.mgh.harvard.edu> > > > > > > > > > > > Phone Number: 617-724-2358 > > > > > > > > > > > Fax: 617-726-7422 > > > > > > > > > > > > > > > > > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > > > > > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > > > > > > > > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html (http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html) > > > > > > > > > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > > > > > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > > > > > > > Outgoing: > > > > > > > > > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > > > > > Freesurfer mailing list > > > > > > > > > > > Freesurfer(a)nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) > > > > > > > > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > > > > > > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > > > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > > > > Freesurfer mailing list > > > > > > > > > > Freesurfer(a)nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) > > > > > > > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > > > > > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > > > Freesurfer mailing list > > > > > > > > > Freesurfer(a)nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) > > > > > > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > > > > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > > > > > > > > The information in this e-mail is intended only for the person to > > > > > > > > > whom it is > > > > > > > > > addressed. If you believe this e-mail was sent to you in error and > > > > > > > > > the e-mail > > > > > > > > > contains patient information, please contact the Partners Compliance > > > > > > > > > HelpLine at > > > > > > > > > http://www.partners.org/complianceline . If the e-mail was sent to > > > > > > > > > you in error > > > > > > > > > but does not contain patient information, please contact the sender > > > > > > > > > and properly > > > > > > > > > dispose of the e-mail. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > Freesurfer mailing list > > > > > > > Freesurfer(a)nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > Douglas N. Greve, Ph.D. > > > > > > MGH-NMR Center > > > > > > greve(a)nmr.mgh.harvard.edu (mailto:greve@nmr.mgh.harvard.edu) <mailto:greve@nmr.mgh.harvard.edu> > > > > > > Phone Number: 617-724-2358 > > > > > > Fax: 617-726-7422 > > > > > > > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > > > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html (http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html) > > > > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > > > > > > > > _______________________________________________ > > > > > > Freesurfer mailing list > > > > > > Freesurfer(a)nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer(a)nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > > > -- > > > > Douglas N. Greve, Ph.D. > > > > MGH-NMR Center > > > > greve(a)nmr.mgh.harvard.edu (mailto:greve@nmr.mgh.harvard.edu) > > > > Phone Number: 617-724-2358 > > > > Fax: 617-726-7422 > > > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html (http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html) > > > > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > The information in this e-mail is intended only for the person to whom it is > > addressed. If you believe this e-mail was sent to you in error and the e-mail > > contains patient information, please contact the Partners Compliance HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to you in error > > but does not contain patient information, please contact the sender and properly > > dispose of the e-mail. > > > > > > > >

1 0

using wm edits and control points at the same run
by james pardon 06 Jul '14

06 Jul '14

Hi, In a subject that I need to edit both wm.mgz and add some control points, I'm wondering what is the correct recon-all options so that all changes are applied in on additional run? I noticed that I could overwrite changes made by one or the other if I run them in tandem (and not simultaneously). Thanks James

2 1

webiste is down
by Arman Eshaghi 05 Jul '14

05 Jul '14

Just a heads up that the Freesurfer website is down as of 6:36 am EST 5 July Arman

2 1

mri_convert WARNING: files are not found to be different and cannot be sorted and cannot fit in 256^3 mm^3 volume.
by Knut J Bjuland 05 Jul '14

05 Jul '14

Dear FreeSurfers, I have imported several dicom files with recon-all -i -subjid id. All files were imported correctly, apart from one subjects. When I try to convert it direcelty with mri_convert -ot mgz dicom/9999/1.dcm -s 9999 I get this error message. WARNING: files are not found to be different and cannot be sorted File1: ../../../../dicom/9999/162.dcm File2: ../../../../dicom/9999/2.dcm When I process the subject with recon-all -s 9999 -all. I got this message. WARNING ==================++++++++++++++++++++++++======================================= The physical sizes are (240.00 mm, 240.00 mm, 384.00 mm), which cannot fit in 256^3 mm^3 volumes. The resulting volume will have 384 slices. If you find problems, please let us know (freesurfer(a)nmr.mgh.harvard.edu) Can you please advise me how to import the dicom files? Should I convert them to nifti. Will this affect the end results compared to the other subjects that were imported correctly? Knut J

2 5

Edit Recommendations
by Erik Kastman 05 Jul '14

05 Jul '14

Hi all, I’ve searched the edit tutorials for examples of the surface recon problem in the attached screenshots, but couldn’t find anything close. The problem is a jagged pial surface in only one plane - it seems to occur where gyri are very close together and doesn’t look like a problem in the other two planes. Any recommendations on how to fix this? Or is it not something to worry about? Thanks in advance, Erik Kastman

2 1

Tracula ERROR: fMRIframe: frame >= nframes
by Jun Shinozaki 04 Jul '14

04 Jul '14

Dear All, I am trying to run a single subject in TRACULA (trac-all -prep -c dmrirc), but exited with ERRORS. ERROR: fMRIframe: frame >= nframes The attached file is a log file. Can anyone help me? Thank you in advance. Regards, Jun Shinozaki.

3 13

Re: [Freesurfer] Base Misalignment during Longitudinal Image Processing
by Martin Reuter 04 Jul '14

04 Jul '14

Hi xuan, You can try freesurfer 5.3 for the base creation and see if that fixes it. If not, send me the two norm.mgz of the cross time points and I take a look. Thanks, martin Sent via my smartphone, please excuse brevity. -------- Original message -------- From: XUAN AMELIA TRAN <tranx(a)ucla.edu> Date:07/04/2014 4:00 AM (GMT+01:00) To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] Base Misalignment during Longitudinal Image Processing Hi there, I used inputs from two time points that have been processed with Freesurfer 5.0.0 cross-sectional pipeline. I used the following command to create the base template (using Freesurfer 5.0.0): recon-all -base <templateid> -tp <tp1id> -tp <tp2id> -all The job log said the run was successful. However when inspected with freeview, the norm.mgz for base output shows misalignment (see image attached). Does anyone know how to fix this problem? Thank you! Xuan

1 0

Base Misalignment during Longitudinal Image Processing
by XUAN AMELIA TRAN 03 Jul '14

03 Jul '14

Hi there, I used inputs from two time points that have been processed with Freesurfer 5.0.0 cross-sectional pipeline. I used the following command to create the base template (using Freesurfer 5.0.0): recon-all -base <templateid> -tp <tp1id> -tp <tp2id> -all The job log said the run was successful. However when inspected with freeview, the norm.mgz for base output shows misalignment (see image attached). Does anyone know how to fix this problem? Thank you! Xuan

1 0

Voxels included in wm.mgz but not in white matter surface
by james pardon 03 Jul '14

03 Jul '14

Hi, I'm working on some subjects with gray matter lesions, where usually these lesions happen at the boundary of GM and WM (mostly patients with MS). The problem is that Freesurfer can not follow the cortex past this areas. I have tried to use control points, white matter edits and even editing the problematic regions on orig.mgz volume with neighboring voxels and re running recon-all. My results have improved substantially, however I still have a problem where after white matter edit, and adding some new voxels to wm.mgz, the wm surface (and overlying pial surface) does not respect the wm.mgz. In the attached screenshot for example, I can see some areas that are part of wm.mgz (in red) but not included in WM surface. I was wondering whether anyone can give a hint on what recon-all steps I might need to re-run? Thanks James

2 1

talairach fixes
by Elissa McIntosh 03 Jul '14

03 Jul '14

Hello freesurfer experts, I have two questions. First, I've come across some of my subjects who have crooked alignment on the horizontal view, but have seemingly good talairach results. Does it matter that the alignment is crooked as long as talairach is good? My second question is how off does a talairach have to be to merit a manual fix? I've attached an image of someone whose talairach is slightly off making the green line go outside the brain more than it usually does. But I don't know if I'll do more harm by adjusting it slightly. On a related note, does it matter that the green line seems to go outside the brain in the moveable image? Where the green line extends beyond I've had to make manual edits in most of my subjects. Thank you!

1 0

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